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Article ; Online: Antibody Response to COVID-19 Vaccination in Adults With Hematologic Malignant Disease.

Ollila, Thomas A / Lu, Shaolei / Masel, Rebecca / Zayac, Adam / Paiva, Kimberly / Rogers, Ralph D / Olszewski, Adam J

JAMA oncology

2021 Volume 7, Issue 11, Page(s) 1714–1716

MeSH term(s)	Adult ; Antibody Formation ; COVID-19/immunology ; COVID-19/prevention & control ; COVID-19 Vaccines/immunology ; Hematologic Diseases/immunology ; Humans ; Neoplasms/immunology ; Vaccination
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2021-10-13
Publishing country	United States
Document type	Journal Article
ISSN	2374-2445
ISSN (online)	2374-2445
DOI	10.1001/jamaoncol.2021.4381
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Article ; Online: Seroconversion and outcomes after initial and booster COVID-19 vaccination in adults with hematologic malignancies.

Ollila, Thomas A / Masel, Rebecca H / Reagan, John L / Lu, Shaolei / Rogers, Ralph D / Paiva, Kimberly J / Taher, Rashida / Burguera-Couce, Ella / Zayac, Adam S / Yakirevich, Inna / Niroula, Rabin / Barth, Peter / Olszewski, Adam J

Cancer

2022 Volume 128, Issue 18, Page(s) 3319–3329

Abstract: Background: Patients with hematologic malignancies have impaired humoral immunity secondary to their malignancy and its treatment, placing them at risk of severe coronavirus disease-19 (COVID-19) infection and reduced response to vaccination.: Methods! ...

Abstract	Background: Patients with hematologic malignancies have impaired humoral immunity secondary to their malignancy and its treatment, placing them at risk of severe coronavirus disease-19 (COVID-19) infection and reduced response to vaccination. Methods: The authors retrospectively analyzed serologic responses to initial and booster COVID-19 vaccination in 378 patients with hematologic malignancy and subsequently tracked COVID-19-related outcomes. Results: Seroconversion occurred in 181 patients (48%) after initial vaccination; patients who had active malignancy or those who were recently treated with a B-cell-depleting monoclonal antibody had the lowest rates of seroconversion. For initial nonresponders to vaccination, seroconversion after a booster dose occurred in 48 of 85 patients (56%). The seroconversion rate after the booster was similar for patients on (53%) and off (58%) active therapy (p = .82). Thirty-three patients (8.8%) developed a COVID-19 infection, and there were three COVID-19-related deaths (0.8%). Although no significant association was observed between postvaccination seroconversion and the incidence of COVID-19 infection, no patient with seroconversion died from COVID-19, and no patient who received tixagevimab/cilgavimab (N = 25) was diagnosed with a COVID-19 infection. Conclusions: Booster vaccinations can promote seroconversion in a significant proportion of patients who are seronegative after the initial vaccination course regardless of the specific vaccine or on/off treatment status at the time of revaccination. Although postvaccination seroconversion may not be associated with a decrease in any (including asymptomatic) COVID-19 infection, the authors' experience suggested that effective vaccination (including a booster), supplemented by passive immunization using tixagevimab/cilgavimab in case of lack of seroconversion, effectively eliminated the risk of COVID-19 death in the otherwise high-risk population. Lay summary: Patients with hematologic malignancy, especially lymphoma, have an impaired response to coronavirus disease 2019 (COVID-19) vaccination. In this single-institution review, less than one half of the patients studied made detectable antibodies. For those who did not make detectable antibodies after initial vaccination, over one half (65%) were able to produce antibodies after booster vaccination. By the end of February 2022, 33 of the original 378 patients had a documented COVID-19 infection. The only deaths from COVID-19 were in those who had undetectable antibodies, and no patient who received prophylactic antibody therapy developed a COVID-19 infection.
MeSH term(s)	Adult ; Antibodies, Monoclonal ; Antibodies, Viral ; COVID-19 ; COVID-19 Vaccines ; Hematologic Neoplasms ; Hepatitis B Vaccines ; Humans ; Retrospective Studies ; Seroconversion ; Vaccination
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Viral ; COVID-19 Vaccines ; Hepatitis B Vaccines ; tixagevimab ; cilgavimab (1KUR4BN70F)
Language	English
Publishing date	2022-07-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1429-1
ISSN	1097-0142 ; 0008-543X ; 1934-662X
ISSN (online)	1097-0142
ISSN	0008-543X ; 1934-662X
DOI	10.1002/cncr.34354
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Article ; Online: Evaluation of BioPlex 2200 Syphilis Total With Automated Rapid Plasma Reagin: Experience From a Tertiary Medical Center.

Tang, Eric W / Paiva, Kimberly J / Pytel-Parenteau, Diane L / Maynard, Michaela A / Chan, Philip A / Lu, Shaolei

Sexually transmitted diseases

2020 Volume 47, Issue 5, Page(s) 301–305

Abstract: Background: Treponema-specific assays are widely adopted in the first step of the reverse algorithm of serologic syphilis screening. The new BioPlex 2200 Syphilis Total and rapid plasma reagin (RPR) test is designed to perform the first 2 steps of the ... ...

Abstract	Background: Treponema-specific assays are widely adopted in the first step of the reverse algorithm of serologic syphilis screening. The new BioPlex 2200 Syphilis Total and rapid plasma reagin (RPR) test is designed to perform the first 2 steps of the algorithm simultaneously. However, limited data regarding the BioPlex Syphilis Total and RPR in clinical practice exist. Methods: A total of 293 random samples at a tertiary medical center were tested by BioPlex Syphilis Total and RPR, BioPlex Syphilis IgG, Architect Syphilis TP, and BD Macro-Vue RPR card. Treponema pallidum particle agglutination (TP-PA) assay and clinical chart review were used to resolve discrepancies. Comparisons were performed among treponemal-specific assays and between 2 RPR tests. Results: Good overall agreements (>91%) were achieved between BioPlex Syphilis Total, BioPlex Syphilis IgG, and Architect Syphilis TP. Overall agreement between BioPlex RPR and BD RPR was 86.8% with positive percent agreement of 66.7% and negative percent agreement of 96.3%. There were 37 discordant samples including 30 with BD RPR+/BioPlex RPR- and 7 with BD RPR-/BioPlex RPR+. Negative BioPlex RPR results were observed in samples with reactive BD RPR: 10 (91%) of 11 for BD RPR 1:1, 13 (65%) of 20 for BD RPR 1:2, 6 (35%) of 17 for BD RPR 1:4, and 1 (7%) of 14 for BD RPR 1:8. The discordant samples were predominantly from patients with high-risk of syphilis reinfection and included 9 patients with an early reinfection. Conclusions: Our results demonstrated that BioPlex Syphilis Total and Architect Syphilis TP performed similarly. The BioPlex RPR missed a small number of early syphilis reinfections, and its implementation should depend on the patient population that the laboratory serves.
MeSH term(s)	Antibodies, Bacterial ; Humans ; Immunoassay/methods ; Predictive Value of Tests ; Reagins/blood ; Reproducibility of Results ; Sensitivity and Specificity ; Syphilis/blood ; Syphilis/diagnosis ; Syphilis/epidemiology ; Syphilis Serodiagnosis/methods ; Treponema pallidum/immunology ; Treponema pallidum/isolation & purification ; United States
Chemical Substances	Antibodies, Bacterial ; Reagins
Language	English
Publishing date	2020-02-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	435191-5
ISSN	1537-4521 ; 0148-5717
ISSN (online)	1537-4521
ISSN	0148-5717
DOI	10.1097/OLQ.0000000000001153
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Article ; Online: Validation and performance comparison of three SARS-CoV-2 antibody assays.

Paiva, Kimberly J / Grisson, Ricky D / Chan, Philip A / Huard, Richard C / Caliendo, Angela M / Lonks, John R / King, Ewa / Tang, Eric W / Pytel-Parenteau, Diane L / Nam, Ga H / Yakirevich, Evgeny / Lu, Shaolei

Journal of medical virology

2020 Volume 93, Issue 2, Page(s) 916–923

Abstract: Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of coronavirus disease 2019 (COVID-19), although its clinical and epidemiologic utilities are still debatable. ... ...

Abstract	Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of coronavirus disease 2019 (COVID-19), although its clinical and epidemiologic utilities are still debatable. Characterizing these assays provides scientific basis to best use them. The current study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo total antibody test) using 113 blood samples from 71 PCR-confirmed COVID-19 hospitalized patients, 119 samples with potential cross-reactions, and 1068 negative controls including 942 pre-pandemic samples. SARS-CoV-2 IgM antibodies became detectable 3-4 days post-symptom onset using SQ IgM test and IgG antibodies were first detected 5-6 days post-onset using SQ IgG. Abbott IgG and Wondfo Total were able to detect antibodies 7 to 8 days post-onset. After 14 days post-symptom onset, the SQ IgG, Abbott IgG and Wondfo Total tests were able to detect antibodies from 100% of the PCR-confirmed patients in this series; 87.5% sensitivity for SQ IgM. Overall agreement was 88.5% between SQ IgM/IgG and Wondfo Total and 94.6% between SQ IgG and Abbott IgG. No cross-reaction due to recent sera with three of the endemic coronaviruses was observed. Viral hepatitis and autoimmune samples were the main source of limited cross-reactions. The specificities were 100% for SQ IgG and Wondfo Total, 99.62% for Abbott IgG, and 98.87% for SQ IgM. These findings demonstrated high sensitivity and specificity of appropriately validated SARS-CoV-2 serologic assays with implications for clinical use and epidemiological seroprevalence studies.
MeSH term(s)	Aged ; Antibodies, Viral/blood ; COVID-19/diagnosis ; COVID-19/immunology ; COVID-19 Serological Testing/methods ; Cross Reactions ; Female ; Humans ; Immunoassay/methods ; Immunoglobulin G/blood ; Immunoglobulin M/blood ; Luminescent Measurements/methods ; Male ; Middle Aged ; Reagent Kits, Diagnostic ; Sensitivity and Specificity
Chemical Substances	Antibodies, Viral ; Immunoglobulin G ; Immunoglobulin M ; Reagent Kits, Diagnostic
Keywords	covid19
Language	English
Publishing date	2020-08-13
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Validation Study
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.26341
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Article ; Online: Validation and performance comparison of three SARS‐CoV‐2 antibody assays

Paiva, Kimberly J. / Grisson, Ricky D. / Chan, Philip A. / Huard, Richard C. / Caliendo, Angela M. / Lonks, John R. / King, Ewa / Tang, Eric W. / Pytel‐Parenteau, Diane L. / Nam, Ga H. / Yakirevich, Evgeny / Lu, Shaolei

Journal of Medical Virology ; ISSN 0146-6615 1096-9071

2020

Keywords	Virology ; Infectious Diseases ; covid19
Language	English
Publisher	Wiley
Publishing country	us
Document type	Article ; Online
DOI	10.1002/jmv.26341
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Validation and Performance Comparison of Three SARS-CoV-2 Antibody Assays

Lu, Shaolei / Paiva, Kimberly J / Grisson, Ricky D / Chan, Philip A / Lonks, John / King, Ewa / Huard, Richard C / Pytel-Parenteau, Diane L / Nam, Ga Hie / Yakirevich, Evgeny

bioRxiv

Abstract: Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of Coronavirus Disease 2019 (COVID-19). The clinical and epidemiologic utilities of antibody-based SARS-CoV-2 testing ... ...

Abstract	Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of Coronavirus Disease 2019 (COVID-19). The clinical and epidemiologic utilities of antibody-based SARS-CoV-2 testing are under debate. Characterizing these assays helps to understand the disease and provide scientific basis to decide how to best use these assays. The study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo Total Antibody Test). Validation included 113 blood samples from 71 PCR-confirmed COVID-19 patients and 1182 samples from negative controls and interferences/cross-reactions, including 1063 pre-pandemic samples. IgM antibodies against SARS-CoV-2 were detected as early as post-symptom onset days 3-4. IgG antibodies were first detected post-onset days 5-6 by SQ assays. The detection rates increased gradually, and SQ IgG, Abbott IgG and Wondfo Total detected antibodies from all the PCR-confirmed patients 14 days after symptom onset. Overall agreements between SQ IgM/IgG and Wondfo Total reached 88.5% and 94.6% between SQ IgG and Abbott IgG (Kappa = 0.75, 0.89). No cross-reaction with other endemic coronavirus infections were identified. Viral hepatitis and autoimmune samples were the main cross-reactions observed. However, the interferences/cross-reactions were low. The specificities were 100% for SQ IgG and Wondfo Total and 99.62% for Abbott IgG and 98.87% for SQ IgM. These findings demonstrate high sensitivity and specificity of appropriately validated antibody-based SARS-CoV-2 assays with implications for clinical use and epidemiological seroprevalence studies.
Keywords	covid19
Language	English
Publishing date	2020-05-30
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.05.29.124776
Database	COVID19

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Article: Validation and performance comparison of three SARS-CoV-2 antibody assays

J. med. virol

Abstract	Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of coronavirus disease 2019 (COVID-19), although its clinical and epidemiologic utilities are still debatable. Characterizing these assays provides scientific basis to best use them. The current study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo total antibody test) using 113 blood samples from 71 PCR-confirmed COVID-19 hospitalized patients, 119 samples with potential cross-reactions, and 1068 negative controls including 942 pre-pandemic samples. SARS-CoV-2 IgM antibodies became detectable 3-4 days post-symptom onset using SQ IgM test and IgG antibodies were first detected 5-6 days post-onset using SQ IgG. Abbott IgG and Wondfo Total were able to detect antibodies 7 to 8 days post-onset. After 14 days post-symptom onset, the SQ IgG, Abbott IgG and Wondfo Total tests were able to detect antibodies from 100% of the PCR-confirmed patients in this series; 87.5% sensitivity for SQ IgM. Overall agreement was 88.5% between SQ IgM/IgG and Wondfo Total and 94.6% between SQ IgG and Abbott IgG. No cross-reaction due to recent sera with three of the endemic coronaviruses was observed. Viral hepatitis and autoimmune samples were the main source of limited cross-reactions. The specificities were 100% for SQ IgG and Wondfo Total, 99.62% for Abbott IgG, and 98.87% for SQ IgM. These findings demonstrated high sensitivity and specificity of appropriately validated SARS-CoV-2 serologic assays with implications for clinical use and epidemiological seroprevalence studies.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #671278
Database	COVID19

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Article ; Online: Validation and Performance Comparison of Three SARS-CoV-2 Antibody Assays

Paiva, Kimberly J / Grisson, Ricky D / Chan, Philip A / Lonks, John R. / King, Ewa / Huard, Richard C / Pytel-Parenteau, Diane L / Nam, Ga Hie / Yakirevich, Evgeny / Lu, Shaolei

bioRxiv

Abstract	Serology testing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly being used during the current pandemic of Coronavirus Disease 2019 (COVID-19). The clinical and epidemiologic utilities of antibody-based SARS-CoV-2 testing are under debate. Characterizing these assays helps to understand the disease and provides scientific basis for deciding how to best use these assays. The study assessed one chemiluminescent assay (Abbott COVID-2 IgG) and two lateral flow assays (STANDARD Q [SQ] IgM/IgG Duo and Wondfo Total Antibody Test). Validation included 113 blood samples from 71 PCR-confirmed COVID-19 patients and 1182 samples from negative controls with potential interferences/cross-reactions, including 1063 pre-pandemic samples. IgM antibodies against SARS-CoV-2 were detected as early as post-symptom onset days 3-4. IgG antibodies were first detected post-onset days 5-6 by SQ assays. The detection rates increased gradually, and SQ IgG, Abbott IgG and Wondfo Total detected antibodies from all the PCR-confirmed patients 14 days after symptom onset. Overall agreements between SQ IgM/IgG and Wondfo Total was 88.5% and between SQ IgG and Abbott IgG was 94.6% (Kappa = 0.75, 0.89). No cross-reaction with other endemic coronavirus infections were identified. Viral hepatitis and autoimmune samples were the main cross-reactions observed. However, the interferences/cross-reactions were low. The specificities were 100% for SQ IgG and Wondfo Total and 99.62% for Abbott IgG and 98.87% for SQ IgM. These findings demonstrate high sensitivity and specificity of appropriately validated antibody-based SARS-CoV-2 assays with implications for clinical use and epidemiological seroprevalence studies.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.05.29.124776
Database	COVID19

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Article ; Online: Hesperidin Promotes Osteogenesis and Modulates Collagen Matrix Organization and Mineralization In Vitro and In Vivo.

Miguez, Patricia A / Tuin, Stephen A / Robinson, Adam G / Belcher, Joyce / Jongwattanapisan, Prapaporn / Perley, Kimberly / de Paiva Gonҫalves, Vinicius / Hanifi, Arash / Pleshko, Nancy / Barton, Elisabeth R

International journal of molecular sciences

2021 Volume 22, Issue 6

Abstract: This study evaluated the direct effect of a phytochemical, hesperidin, on pre-osteoblast cell function as well as osteogenesis and collagen matrix quality, as there is little known about hesperidin's influence in mineralized tissue formation and ... ...

Abstract	This study evaluated the direct effect of a phytochemical, hesperidin, on pre-osteoblast cell function as well as osteogenesis and collagen matrix quality, as there is little known about hesperidin's influence in mineralized tissue formation and regeneration. Hesperidin was added to a culture of MC3T3-E1 cells at various concentrations. Cell proliferation, viability, osteogenic gene expression and deposited collagen matrix analyses were performed. Treatment with hesperidin showed significant upregulation of osteogenic markers, particularly with lower doses. Mature and compact collagen fibrils in hesperidin-treated cultures were observed by picrosirius red staining (PSR), although a thinner matrix layer was present for the higher dose of hesperidin compared to osteogenic media alone. Fourier-transform infrared spectroscopy indicated a better mineral-to-matrix ratio and matrix distribution in cultures exposed to hesperidin and confirmed less collagen deposited with the 100-µM dose of hesperidin. In vivo, hesperidin combined with a suboptimal dose of bone morphogenetic protein 2 (BMP2) (dose unable to promote healing of a rat mandible critical-sized bone defect) in a collagenous scaffold promoted a well-controlled (not ectopic) pattern of bone formation as compared to a large dose of BMP2 (previously defined as optimal in healing the critical-sized defect, although of ectopic nature). PSR staining of newly formed bone demonstrated that hesperidin can promote maturation of bone organic matrix. Our findings show, for the first time, that hesperidin has a modulatory role in mineralized tissue formation via not only osteoblast cell differentiation but also matrix organization and matrix-to-mineral ratio and could be a potential adjunct in regenerative bone therapies.
MeSH term(s)	Animals ; Bone Morphogenetic Protein 2/pharmacology ; Bone Regeneration ; Calcification, Physiologic/drug effects ; Cell Line ; Cells, Cultured ; Collagen/metabolism ; Extracellular Matrix/metabolism ; Hesperidin/pharmacology ; Mice ; Osteoblasts/drug effects ; Osteoblasts/metabolism ; Osteogenesis/drug effects ; Rats
Chemical Substances	Bmp2 protein, mouse ; Bone Morphogenetic Protein 2 ; Collagen (9007-34-5) ; Hesperidin (E750O06Y6O)
Language	English
Publishing date	2021-03-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22063223
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Article ; Online: The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

Walker, Kimberly / Kalra, Divya / Lowdon, Rebecca / Chen, Guangyi / Molik, David / Soto, Daniela C / Dabbaghie, Fawaz / Khleifat, Ahmad Al / Mahmoud, Medhat / Paulin, Luis F / Raza, Muhammad Sohail / Pfeifer, Susanne P / Agustinho, Daniel Paiva / Aliyev, Elbay / Avdeyev, Pavel / Barrozo, Enrico R / Behera, Sairam / Billingsley, Kimberley / Chong, Li Chuin /

Choubey, Deepak / De Coster, Wouter / Fu, Yilei / Gener, Alejandro R / Hefferon, Timothy / Henke, David Morgan / Höps, Wolfram / Illarionova, Anastasia / Jochum, Michael D / Jose, Maria / Kesharwani, Rupesh K / Kolora, Sree Rohit Raj / Kubica, Jędrzej / Lakra, Priya / Lattimer, Damaris / Liew, Chia-Sin / Lo, Bai-Wei / Lo, Chunhsuan / Lötter, Anneri / Majidian, Sina / Mendem, Suresh Kumar / Mondal, Rajarshi / Ohmiya, Hiroko / Parvin, Nasrin / Peralta, Carolina / Poon, Chi-Lam / Prabhakaran, Ramanandan / Saitou, Marie / Sammi, Aditi / Sanio, Philippe / Sapoval, Nicolae / Syed, Najeeb / Treangen, Todd / Wang, Gaojianyong / Xu, Tiancheng / Yang, Jianzhi / Zhang, Shangzhe / Zhou, Weiyu / Sedlazeck, Fritz J / Busby, Ben

F1000Research

2022 Volume 11, Page(s) 530

Abstract: In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants ( ...

Abstract	In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19 ; Genomics ; Software
Language	English
Publishing date	2022-05-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2699932-8
ISSN	2046-1402 ; 2046-1402
ISSN (online)	2046-1402
ISSN	2046-1402
DOI	10.12688/f1000research.110194.1
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